Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate WP_010961434.1 MCA_RS10785 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P58350 (410 letters) >NCBI__GCF_000008325.1:WP_010961434.1 Length = 393 Score = 383 bits (984), Expect = e-111 Identities = 200/394 (50%), Positives = 260/394 (65%), Gaps = 6/394 (1%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R+ SI S L + ARAAAM+ GK ++ LGAGEPDFDTP+H+KQAA AI +G TKY Sbjct: 6 SDRVQSIKPSPTLAVTARAAAMRAAGKDIVGLGAGEPDFDTPDHIKQAAIQAIEKGFTKY 65 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 TA+DGTP LK+AI+ KF+RENGL Y LD+I V+ G KQ +N A L+PGDEV+IP PY Sbjct: 66 TAVDGTPGLKQAIQAKFKRENGLDYALDQILVSCGGKQSFYNLAQALLNPGDEVVIPAPY 125 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY D+V + PV++ F++T +LEAA+T RTR ++NSPSNP+G AY+A Sbjct: 126 WVSYPDMVLLAGAVPVIVEAGQQQAFKITPAQLEAALTARTRLFVINSPSNPTGMAYTAE 185 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + L EVL R P V + DDMYEHI+++G F + P L RT+ +NGVSKAY+MT Sbjct: 186 ELAGLGEVLRRFPEVVIATDDMYEHILWEG-GFSNVLNVCPDLYERTVVLNGVSKAYSMT 244 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWRIGYA GP LI+AM +QSQ+TS P+SISQ A+ AALNG Q F+ E+F++R D Sbjct: 245 GWRIGYAAGPERLIEAMTNIQSQSTSNPTSISQVAAEAALNGEQGFIAGMVEAFKQRHDF 304 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 VV LNAI G+DC G FY + ++ + D YL+E VAVVP Sbjct: 305 VVGRLNAIPGVDCLKTHGTFYVLPNVEAAMARL-----HLADDVALSEYLIEQGGVAVVP 359 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIAAACDR 408 GSAFG R+S ATS A L++A+ER+A + Sbjct: 360 GSAFGAPGHVRLSIATSMANLEKAMERLATTLSK 393 Lambda K H 0.318 0.134 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 463 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 410 Length of database: 393 Length adjustment: 31 Effective length of query: 379 Effective length of database: 362 Effective search space: 137198 Effective search space used: 137198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory